I seem to remember this being suggested before, a "selective clearing" feature. I agree it would be great. When I'm traveling and don't have good connectivity (or a lot of time) I try to only read things that look interesting from the Newest Nodes page. But normally I don't have the time in a single sitting to read all of the interesting parts, yet it would be nice to be able to remove stuff I'm not going to read from the list, to prevent it from growing uncontrollably.
in reply to 'Clear Flag' Proofing
Now, as others have pointed, I don't know how hard this would be to implement. I suspect that right now there is a date stamp for each user which marks the latest article read, and this feature would require one flag per article, so I suspect it would indeed be quite hard.
I'll only add that if this feature were ever to be implemented, having "Clear all checkboxes" and "Set all checkboxes" buttons would be very valuable, to be able to do both "clear all except these" or "clear only these" behaviors.